3zdg

Crystal Structure of Ls-AChBP complexed with carbamoylcholine analogue 3-(dimethylamino)butyl dimethylcarbamate (DMABC)

Method: X-RAY DIFFRACTION Dmax: 172.1 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

ACETYLCHOLINE BINDING PROTEIN

LYMNAEA STAGNALIS

UniProt P58154

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain K; UniProt 20–229 Chain L; UniProt 20–229 Chain M; UniProt 20–229 Chain N; UniProt 20–229 Chain O; UniProt 20–229 Not recorded XRX 3-(dimethylamino)butyl dimethylcarbamate × 5 SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.1 M TRIS (AT PH 8.5 ), 2.0 M AMMONIUM SULPHATE Resolution 2.48 Å R-free 0.221
2 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 20–229 Chain B; UniProt 20–229 Chain C; UniProt 20–229 Chain D; UniProt 20–229 Chain E; UniProt 20–229 Not recorded XRX 3-(dimethylamino)butyl dimethylcarbamate × 5 SO4 SULFATE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.1 M TRIS (AT PH 8.5 ), 2.0 M AMMONIUM SULPHATE Resolution 2.48 Å R-free 0.221
3 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 20–229 Chain G; UniProt 20–229 Chain H; UniProt 20–229 Chain I; UniProt 20–229 Chain J; UniProt 20–229 Not recorded XRX 3-(dimethylamino)butyl dimethylcarbamate × 5 SO4 SULFATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.1 M TRIS (AT PH 8.5 ), 2.0 M AMMONIUM SULPHATE Resolution 2.48 Å R-free 0.221
4 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain P; UniProt 20–229 Chain Q; UniProt 20–229 Chain R; UniProt 20–229 Chain S; UniProt 20–229 Chain T; UniProt 20–229 Not recorded XRX 3-(dimethylamino)butyl dimethylcarbamate × 5 SO4 SULFATE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.1 M TRIS (AT PH 8.5 ), 2.0 M AMMONIUM SULPHATE Resolution 2.48 Å R-free 0.221

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

59 other PDB entries and 119 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACHP_LYMST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–210; UniProt 20–229 Author chain B; PDBConstruct 1–210; UniProt 20–229 Author chain C; PDBConstruct 1–210; UniProt 20–229 Author chain D; PDBConstruct 1–210; UniProt 20–229 Author chain E; PDBConstruct 1–210; UniProt 20–229 Author chain F; PDBConstruct 1–210; UniProt 20–229 Author chain G; PDBConstruct 1–210; UniProt 20–229 Author chain H; PDBConstruct 1–210; UniProt 20–229 Author chain I; PDBConstruct 1–210; UniProt 20–229 Author chain J; PDBConstruct 1–210; UniProt 20–229 Author chain K; PDBConstruct 1–210; UniProt 20–229 Author chain L; PDBConstruct 1–210; UniProt 20–229 Author chain M; PDBConstruct 1–210; UniProt 20–229 Author chain N; PDBConstruct 1–210; UniProt 20–229 Author chain O; PDBConstruct 1–210; UniProt 20–229 Author chain P; PDBConstruct 1–210; UniProt 20–229 Author chain Q; PDBConstruct 1–210; UniProt 20–229 Author chain R; PDBConstruct 1–210; UniProt 20–229 Author chain S; PDBConstruct 1–210; UniProt 20–229 Author chain T; PDBConstruct 1–210; UniProt 20–229

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3zdg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3zdg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3zdg
Deposition date deposition_date2012-11-26
Structure title titleCrystal Structure of Ls-AChBP complexed with carbamoylcholine analogue 3-(dimethylamino)butyl dimethylcarbamate (DMABC)
Keywords keywordsACETYLCHOLINE-BINDING PROTEIN; ACETYLCHOLINE-BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier57.93
Radius of gyration Rg (electron density) rg_electron57.02
Forward intensity I(0) i03099100000.00
Molecular weight molecular_weight459600.0 kDa
Excluded volume excluded_volume571290 ų
Envelope volume envelope_volume833790 ų
Hydration-shell volume shell_volume118360 ų
Envelope diameter envelope_diameter181.6
Shell Rg shell_rg62.88
Envelope Rg envelope_rg55.30
Shape Rg shape_rg57.01
Total Rg total_rg57.15
Total atoms total_atoms32365
Residues n_residues3991
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax172.1
Rg (real space) rg_real58.06
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real3.0250e+09
I(0) uncertainty (real space) i0_real_error4.8690e+07
Rg (reciprocal space) rg_reciprocal58.19
I(0) (reciprocal space) i0_reciprocal3102000000.0000
Solution quality estimate total_estimate0.6774
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary89.2
Skewness Skewness skewness0.062
Kurtosis Kurtosis kurtosis-0.632
Angular range angular_range— – 0.1350 −1
Current regularization parameter α current_alpha1.7510
Highest regularization parameter α highest_alpha1045000000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.967; Stabil: 0.924; Sysdev: 0.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.170

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd3zdga_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgb_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgc_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgd_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdge_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgf_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgg_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgh_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgi_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgj_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgk_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgl_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgm_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgn_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgo_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgp_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgq_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgr_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgs_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
Domain ID domain_idd3zdgt_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like

CATH v4.4 (20 domains)

Domain ID domain_id3zdgA00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgB00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgC00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgD00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgE00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgF00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgG00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgH00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgI00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgJ00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgK00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgL00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgM00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgN00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgO00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgP00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgQ00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgR00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgS00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3zdgT00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain

8. Citations (1)

9. Files and Curves (10)